Identification of QTLs for rice grain size and shape of Iranian cultivars using SSR markers

Grain size is a main component of rice appearance quality. In this study, we performed the SSR mapping of quantitative trait loci (QTLs) controlling grain size (grain length and breadth) and shape (length/breadth ratio) using an F₂ population of a cross between two Iranian cultivars, Domsephid and Gerdeh, comprising of 192 individuals. A linkage map with 88 markers was constructed, which covered 1367.9 cM of the rice genome with an average distance of 18 cM between markers. Interval mapping procedure was used to identify the QTLs controlling three grain traits, and QTLs detected were further confirmed using composite interval mapping. A total of 11 intervals carrying 18 QTLs for three traits were identifed, that included five QTLs for grain length, seven QTLs for grain breadth, and six QTLs for grain shape. A major QTL for grain length was detected on chromosome 3, that explained 19.3% of the phenotypic variation. Two major QTLs for grain breadth were mapped on chromosomes 3 and 8, which explained 34.1% and 20% of the phenotypic variation, respectively. Another two major QTLs were identified for grain shape on chromosomes 3 and 8, which accounted for 27.1% and 20.5% of the phenotypic variance, respectively. The two QTLs that were mapped for grain shape coincided with the major QTLs detected for grain length and grain breadth. Intrestingly, gs2 QTL specific to grain shape was detected on chromosome 2 that explained 15% of the phenotypic variation.     

Variation of the genomic proportion of the recurrent parent in BC1 and its relation to yield performance in sorghum (Sorghum bicolor) breeding for low-input conditions

In order to define the variation of the genomic proportion of the recurrent parent [G(RP)] and its relation to yield, G(RP) of individual BC₁ plants of two sorghum populations composed of a high‐yielding cultivar as recurrent parent (RP) and a donor with superior drought resistance or grain quality, respectively, was estimated using AFLPs and SSRs. G(RP) in BC₁ ranged from 0.53 to 0.95 and averaged to 0.76 in the population (NP4453 × ‘SV‐2’) × ‘SV‐2’. G(RP) varied between 0.60 and 0.86 and averaged to 0.74 in the BC₁ of (ICV‐219 × ‘SV‐2’) × ‘SV‐2’. Results show that plants with a G(RP) equivalent to BC₂ (0.875) or BC₃ (0.938), respectively, can be selected from BC₁. Yield performance of BC₁S₁ families was tested in field trials carried out in South Africa. The correlation between yield and G(RP) in BC₁ was low. Selection according to G(RP) did not result in an effective preselection for yield.     

Analysis of wheat-Thinopyrum intermedium derivatives with BYDV-resistance

Chromosome compositions of seven lines, derived from hybrids between a wheat cultivar and the wheat-Thinopyrum intermedium addition line Z6, with barley yellow dwarf virus (BYDV) resistance, were determined by genomic in situ hybridization, cytogenetic and SSR assays. The results showed that line N522 was a disomic addition line, lines N420 and N439 were 2Ai-2(2B) chromosome substitution lines, lines N431 and N452 were 2Ai-2(2D) chromosome substitution lines, line N523 was a 2Ai-2S(2D) ditelosomic substitution line, and line N530 was a double ditelosomic line with the mitotic chromosome number of 2n = 40 + 4t. One pair of telosomes in line N530 lacked several proximal SSR markers of chromosome 2AS, but possessed certain terminal markers, which were consistent with an acrocentric structure, and the other pair of chromosome arms were presumably 2Ai-2S telosomes with BYDV-resistance. These wheat-Th. intermedium lines provide useful genetic resources for developing alien chromosome translocation lines.     

Segregation distortion in doubled haploid lines of barley (Hordeum vulgare L.) detected by simple sequence repeat (SSR) markers

A total of 147 simple sequence repeat (SSR) markers (including86 barley and 61 wheat microsatellite markers) were tested for their segregation in a doubled haploid (DH) and an F₂ population of barley. The DH population consisted of 71 doubled haploid lines, developed from F₁ plants of a cross between Tadmor and WI2291using isolated microspore culture technique. A genetic linkage map consisting of 43 microsatellite markers was constructed using the DH population. Particularly on chromosome 4H microsatellite markers showed distorted segregation ratios. Segregation of DH lines based on molecular markers were compared with segregation of 92 F₂ lines from the same cross. The proportion of loci deviating from the expected monogenic segregation ratios in the DH population was significantly higher (19/43loci, 44%) than in the F₂ population (7/43 loci, 16%). The deviation was biased towards the WI2291 parent alleles. In line with this observation, WI2291 was found to perform better than Tadmor in regenerating green plantlets with the isolated microspore-culture technique. This revised version was published online in July 2006 with corrections to the Cover Date.     

利用若干单株混合提取DNA方法进行玉米群体SSR的分析

以金皇后玉米群体90个单株：DNA和6个自交系DNA为供试材料，利用15对SSR引物，比较了同一群体4种DNA样品处理(单株DNA样品、3个单株混合DNA样品、10个单株混合DNA样品、15个单株混合DNA样品)的SSR遗传多态性。结果表明，利用单株DNA样品能获得等位基因数、基因频率、基因型杂合度等较全面的遗传信息，适宜进行单个或少量群体的遗传结构研究，但试验工作量大；利用混合DNA样品所能获得的遗传信息有所减少，比较4种DNA样品处理的检测结果发现，15个单株混合样品的检测结果误差较大，而采用3～10个单株DNA混合的样品基本可以反映出一个群体的等位基因数目和SSR带型的差异，由于试验工作量大大减少，可以应用于较多玉米群体间遗传差异的比较。     

中国辽西地区谷子品种遗传多样性的SSR分析

为研究中国辽西地区谷子品种的遗传差异,本研究利用28对SSR标记对辽西地区8个推广面积较大的优质高产谷子品种(包括7个谷子育成品种和1个农家品种)进行遗传多样性分析。研究结果表明:有14对SSR引物共检测出43个等位变异,平均每对引物检出的等位变异数为3.07,14个位点的平均多态信息量(PIC)为0.485;遗传相似性(GS)的变化范围为0.071 4~0.857 1,平均值为0.601 9。聚类分析发现8个品种可分为两大类,农家种与育成品种朝谷14聚为一类,其他6个育成品种聚为另外一类。SSR标记的指纹图谱表明运用4对引物可将8份地方谷子品种成功区分开。本研究结果可为辽西地区谷子品种的亲本选配和遗传改良提供理论依据。     

The study of introgressive lines of Triticum aestivum × Aegilops speltoides by in situ and SSR analyses

Fluorescence in situ hybridization (FISH) with a genome‐specific repeat, Spelt1, and wheat simple sequence repeat (SSR) markers were used to analyse the chromosome constitution of two Triticum aestivum×Aegilops speltoides introgressive lines. The lines 170/98i and 178/98i carried one and two subtelomeric regions of Ae. speltoides (per haploid genome), respectively, marked by Spelt1 repeats according to FISH data. SSR analysis detected homoeologous substitution of wheat chromosome 7D with Ae. speltoides chromosome 7S in the lines 178/98i and 170/98i as well as the assumed terminal translocation in the short arm of chromosome 3A in the line 178/98i. Anthocyanin pigmentation of the coleoptiles was found in the lines 170/98i and 178/98i and resulted from the 7S (7D) substitution. It was demonstrated that Spelt1 could be effectively used for the rapid identification (without DNA isolation) of terminal translocations of T. aestivum×Ae. speltoides introgressive lines as well as for further analysis of the stability of the hybrid plants.     

Studying genetic relationships among coconut varieties/populations using microsatellite markers

The extent of genetic diversity and the genetic relationships among 94 coconut varieties/populations (51 Talls and 43 Dwarfs) representing the entire geographic range of cultivation/distribution of the coconut was assessed using 12 pairs of coconut micro satellite primers. A high level of genetic diversity was observed in the collection with the mean gene diversity of 0.647±0.139, with that of the mean gene diversity of Talls 0.703±0.125 and 0.374±0.204 of Dwarfs. A phenetic tree based on D_AD genetic distances clustered all the 94 varieties/populations into two main groups, with one group composed of all the Talls from southeast Asia, the Pacific, west coast of Panama, and all Dwarfs and the other of all Talls from south Asia, Africa, and the Indian Ocean coast of Thailand. The allele distribution of Dwarfs highlighted a unique position of Dwarf palms from the Philippines exhibiting as much variation as that in the Tall group. The grouping of all Dwarfs representing the entire geographic distribution of the crop with Talls from southeast Asia and the Pacific and the allele distribution between the Tall and Dwarf suggest that the Dwarfs originated from the Tall forms and that too from the Talls of southeast Asia and the Pacific. Talls from Pacific Islands recorded the highest level of genetic diversity (0.6±0.26) with the highest number of alleles (51) among all the regions. This revised version was published online in August 2006 with corrections to the Cover Date.     

Molecular Analysis of Local Potato Cultivars from Tenerife Island Using Microsatellite Markers

We have used 19 SSR markers to fingerprint 41 local potato cultivars from 10 locations of Tenerife Island. These varieties represent relicts of the early introductions originating from South America and have been characterised previously morphologically and ecophysiologically. The SSR primers generated a varying degree of polymorphisms. A total of 67 alleles were observed, 12 of them were present in all cultivars. Several accession and group specific alleles were detected. Similarity coefficients were computed from the molecular data and cluster analyses were performed. Generally, cultivar groups with identical or related common names showed the same SSR patterns or clustered closely together. According to the molecular patterns misleading or confounded names were evident for four accessions. The dendrogram clusters were generally in good agreement with previous classifications of the accessions as Solanum tuberosum subsp. andigena, S. tuberosum subsp. tuberosum and Solanum chaucha genotypes. However in four cases the molecular patterns showed discrepancies with previous species assignments suggesting the need for a more detailed and comparative study of these accessions.     

Selecting in situ conservation sites for grape genetic resources in the USA

Previously, there has not been any in situ conservation sites for crop germplasm within the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Plant Germplasm System (NPGS). Using morphologic and molecular (SSR markers) techniques, we assessed the genetic variation present in populations of rock grape (Vitis rupestris Scheele), a native American grape species, throughout its range. We identified seven in situ conservation sites for rock grape using a strategy based on morphologic and molecular data, taxonomic information, population size and integrity, and landholder commitment. In collaboration with federal and state landholding agencies, we have established the first NPGS in situ conservation sites for American wild relatives of a crop.